Selecting and using an appropriate structural reliability method is critical for the success of structural reliability analysis and reliability-based design optimization. However, most of existing structural reliability methods are developed and designed for a single limit state function and few methods can be used to simultaneously handle multiple limit state functions in a structural system when the failure probability of each limit state function is of interest, for example, in a reliability-based design optimization loop. This article presents a new method for structural reliability analysis with multiple limit state functions using support vector machine technique. A sole support vector machine surrogate model for all limit state functions is constructed by a multi-input multi-output support vector machine algorithm. Furthermore, this multi-input multi-output support vector machine surrogate model for all limit state functions is only trained from one data set with one calculation process, instead of constructing a series of standard support vector machine models which has one output only. Combining the multi-input multi-output support vector machine surrogate model with direct Monte Carlo simulation, the failure probability of the structural system as well as the failure probability of each limit state function corresponding to a failure mode in the structural system can be estimated. Two examples are used to demonstrate the accuracy and efficiency of the presented method.